Last updated on 2026-09-30 01:55:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.9 | 75.96 | 187.06 | 263.02 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.9 | 57.87 | 147.88 | 205.75 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.9 | 53.00 | 131.74 | 184.74 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.9 | 66.00 | 141.36 | 207.36 | OK | |
| r-devel-windows-x86_64 | 1.0.9 | 88.00 | 311.00 | 399.00 | OK | |
| r-patched-linux-x86_64 | 1.0.9 | 77.52 | 185.85 | 263.37 | OK | |
| r-release-linux-x86_64 | 1.0.9 | 74.01 | 183.92 | 257.93 | OK | |
| r-release-macos-arm64 | 1.0.9 | 15.00 | 53.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 1.0.9 | 54.00 | 239.00 | 293.00 | OK | |
| r-release-windows-x86_64 | 1.0.9 | 88.00 | 238.00 | 326.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.9 | 19.00 | 54.00 | 73.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.0.9 | 52.00 | 206.00 | 258.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.9 | 114.00 | 290.00 | 404.00 | OK |
Version: 1.0.9
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), seed, verbose, as.integer(printevery), as.integer(chain_index))
2: horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain)
3: eval(c.expr, envir = args, enclos = envir)
4: eval(c.expr, envir = args, enclos = envir)
Traceback:
1: 5: doTryCatch(return(expr), name, parentenv, handler)cpp_horseshoe(X, Y, intercept, as.integer(nburn), as.integer(npost), seed, verbose, as.integer(printevery), as.integer(chain_index))
6:
2: tryCatchOne(expr, names, parentenv, handlers[[1L]])horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn,
npost = npost, seed = seed_chain, verbose = output_verbose, 7: tryCatchList(expr, classes, parentenv, handlers) printevery = printevery, chain_index = chain)
8: 3: eval(c.expr, envir = args, enclos = envir)tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
4: 9: FUN(X[[i]], ...)eval(c.expr, envir = args, enclos = envir)
10: 5: doTryCatch(return(expr), name, parentenv, handler)
lapply(X = S, FUN = FUN, ...) 6:
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchList(expr, classes, parentenv, handlers)12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)13:
tryCatchList(expr, classes, parentenv, handlers) 9:
FUN(X[[i]], ...)
10: 14: tryCatch(expr, error = function(e) {lapply(X = S, FUN = FUN, ...)
call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) 11: doTryCatch(return(expr), name, parentenv, handler)
call <- sys.call(-4L)12: dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste("Error in", dcall, ": ")
13: tryCatchList(expr, classes, parentenv, handlers) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")14: tryCatch(expr, error = function(e) { if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], call <- conditionCall(e) if (!is.null(call)) { type = "b") if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) if (w > LONG) prefix <- paste0(prefix, "\n ") dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") } else prefix <- "Error : " LONG <- 75L msg <- paste0(prefix, conditionMessage(e), "\n") sm <- strsplit(conditionMessage(e), "\n")[[1L]] .Internal(seterrmessage(msg[1L])) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (!silent && isTRUE(getOption("show.error.messages"))) { if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], cat(msg, file = outFile) type = "b") .Internal(printDeferredWarnings()) if (w > LONG) } prefix <- paste0(prefix, "\n ") invisible(structure(msg, class = "try-error", condition = e)) } else prefix <- "Error : "}) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))15: if (!silent && isTRUE(getOption("show.error.messages"))) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) cat(msg, file = outFile)
.Internal(printDeferredWarnings())16: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) invisible(structure(msg, class = "try-error", condition = e))
})17:
FUN(X[[i]], ...)15:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)18:
lapply(seq_len(cores), inner.do)16:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
19: 17: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores)FUN(X[[i]], ...)
20: 18: e$fun(obj, substitute(ex), parent.frame(), e$data)lapply(seq_len(cores), inner.do)
21: 19: foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores) .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% {
seed_chain = if (!is.null(seed)) 20: seed + chaine$fun(obj, substitute(ex), parent.frame(), e$data) else NULL
return(switch(model, Multi_Laplace = {21: multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, foreach::foreach(chain = 1:nchains, .combine = list, .multicombine = TRUE, v = extra_parameters$v, nburn = nburn, npost = npost, .maxcombine = ifelse(nchains >= 2, nchains, 2)) %dopar% { seed = seed_chain, verbose = output_verbose, printevery = printevery, seed_chain = if (!is.null(seed)) chain_index = chain) seed + chain }, Horseshoe = { else NULL horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, return(switch(model, Multi_Laplace = { npost = npost, seed = seed_chain, verbose = output_verbose, multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, printevery = printevery, chain_index = chain) v = extra_parameters$v, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, }, ARD = { ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, chain_index = chain) npost = npost, seed = seed_chain, verbose = output_verbose, }, Horseshoe = { printevery = printevery, chain_index = chain) horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, }, Spike_Laplace = { npost = npost, seed = seed_chain, verbose = output_verbose, spike_laplace_partially_mcmc(X, Y, intercept = !standardize, printevery = printevery, chain_index = chain) a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, }, ARD = { npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, })) npost = npost, seed = seed_chain, verbose = output_verbose, } printevery = printevery, chain_index = chain)
}, Spike_Laplace = {22: spike_laplace_partially_mcmc(X, Y, intercept = !standardize, withCallingHandlers(expr, warning = function(w) if (inherits(w, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, classes)) tryInvokeRestart("muffleWarning")) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)23: }))suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, }
.multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, 22: nchains, 2)) %dopar% {withCallingHandlers(expr, warning = function(w) if (inherits(w, seed_chain = if (!is.null(seed)) classes)) tryInvokeRestart("muffleWarning")) seed + chain
else NULL23: return(switch(model, Multi_Laplace = {suppressWarnings(foreach::foreach(chain = 1:nchains, .combine = list, multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, .multicombine = TRUE, .maxcombine = ifelse(nchains >= 2, v = extra_parameters$v, nburn = nburn, npost = npost, nchains, 2)) %dopar% { seed = seed_chain, verbose = output_verbose, printevery = printevery, seed_chain = if (!is.null(seed)) chain_index = chain) seed + chain }, Horseshoe = { else NULL horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, return(switch(model, Multi_Laplace = { npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) multi_laplace_mcmc(X, Y, intercept = !standardize, h = extra_parameters$h, }, ARD = { v = extra_parameters$v, nburn = nburn, npost = npost, ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, seed = seed_chain, verbose = output_verbose, printevery = printevery, npost = npost, seed = seed_chain, verbose = output_verbose, chain_index = chain) printevery = printevery, chain_index = chain) }, Horseshoe = { }, Spike_Laplace = { horseshoe_mcmc(X, Y, intercept = !standardize, nburn = nburn, spike_laplace_partially_mcmc(X, Y, intercept = !standardize, npost = npost, seed = seed_chain, verbose = output_verbose, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, npost = npost, seed = seed_chain, verbose = output_verbose, printevery = printevery, chain_index = chain) printevery = printevery, chain_index = chain) }, ARD = { })) ARD_mcmc(X, Y, intercept = !standardize, nburn = nburn, }) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)24: }, Spike_Laplace = {BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe", spike_laplace_partially_mcmc(X, Y, intercept = !standardize, nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, a = extra_parameters$a, b = extra_parameters$b, nburn = nburn, ncores = 2, seed = seed) npost = npost, seed = seed_chain, verbose = output_verbose,
printevery = printevery, chain_index = chain)25: }))eval(expr, envir)})
26: 24: eval(expr, envir)BMI_LASSO(data$data_MI$X, data$data_MI$Y, model = "Horseshoe",
nburn = 4000, npost = 4000, output_verbose = FALSE, nchains = 2, 27: ncores = 2, seed = seed)withVisible(eval(expr, envir))
25: 28: eval(expr, envir)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 26: {eval(expr, envir) watcher$capture_plot_and_output()
if (on_message$capture) {27: watcher$push(cnd)withVisible(eval(expr, envir)) }
if (on_message$silence) {28: invokeRestart("muffleMessage")withCallingHandlers(code, error = function (e) }rlang::entrace(e), message = function (cnd) }, warning = function (cnd) {{ watcher$capture_plot_and_output() if (getOption("warn") >= 2 || getOption("warn") < 0) { if (on_message$capture) { return() watcher$push(cnd) } } watcher$capture_plot_and_output() if (on_message$silence) { if (on_warning$capture) { invokeRestart("muffleMessage") cnd <- sanitize_call(cnd) } watcher$push(cnd)}, warning = function (cnd) }{ if (on_warning$silence) { if (getOption("warn") >= 2 || getOption("warn") < 0) { invokeRestart("muffleWarning") return() } }}, error = function (cnd) watcher$capture_plot_and_output(){ if (on_warning$capture) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$push(cnd) } switch(on_error, continue = invokeRestart("eval_continue"), if (on_warning$silence) { stop = invokeRestart("eval_stop"), error = NULL) invokeRestart("muffleWarning")}) }
}, error = function (cnd) 29: {eval(call) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)30: watcher$push(cnd)eval(call) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)31: })with_handlers({
for (expr in tle$exprs) {29: ev <- withVisible(eval(expr, envir))eval(call) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)30: }eval(call) TRUE
}, handlers)
31: 32: with_handlers({doWithOneRestart(return(expr), restart) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))33: watcher$capture_plot_and_output()withOneRestart(expr, restarts[[1L]]) watcher$print_value(ev$value, ev$visible, envir)
}34: TRUEwithRestartList(expr, restarts[-nr])}, handlers)
35: 32: doWithOneRestart(return(expr), restart)doWithOneRestart(return(expr), restart)
36: 33: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withOneRestart(expr, restarts[[1L]])
37: 34: withRestartList(expr, restarts[-nr])withRestartList(expr, restarts)
35: 38: doWithOneRestart(return(expr), restart)withRestarts(with_handlers({
for (expr in tle$exprs) {36: ev <- withVisible(eval(expr, envir))withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)37: }withRestartList(expr, restarts) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)38:
withRestarts(with_handlers({39: for (expr in tle$exprs) {evaluate::evaluate(...) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()40: watcher$print_value(ev$value, ev$visible, envir)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, } keep_message = if (is.numeric(options$message)) TRUE else options$message, TRUE stop_on_error = if (is.numeric(options$error)) options$error else {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (options$error && options$include)
0L39: else 2Levaluate::evaluate(...) }, output_handler = knit_handlers(options$render, options))
40: 41: in_dir(input_dir(), expr)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 42: stop_on_error = if (is.numeric(options$error)) options$error else {in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (options$error && options$include) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 0L keep_message = if (is.numeric(options$message)) TRUE else options$message, else 2L stop_on_error = if (is.numeric(options$error)) options$error else { }, output_handler = knit_handlers(options$render, options)) if (options$error && options$include)
0L41: else 2Lin_dir(input_dir(), expr)
}, output_handler = knit_handlers(options$render, options)))42:
43: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, eng_r(options) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {44: if (options$error && options$include) block_exec(params) 0L
else 2L45: }, output_handler = knit_handlers(options$render, options)))call_block(x)
43: 46: eng_r(options)process_group(group)
44: 47: block_exec(params)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {45: if (progress && is.function(pb$interrupt)) call_block(x) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)46: })process_group(group)
48: 47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { error = function(e) { if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) pb$interrupt() pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
})49:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 48: error = function(e) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (progress && is.function(pb$interrupt)) error = function(e) { pb$interrupt() if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) pb$interrupt() error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) }), list(rlang_trace_top_env = knit_global())), function(loc) { error <<- format(e) setwd(wd) }), list(rlang_trace_top_env = knit_global())) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 49: paste0("\n", rule(), error, "\n", rule()))xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) error = function(e) {
if (progress && is.function(pb$interrupt)) 50: pb$interrupt()process_file(text, output)
if (is_R_CMD_build() || is_R_CMD_check()) 51: error <<- format(e)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)52: write_utf8(res, output %n% stdout())rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), paste0("\nQuitting from ", loc, if (!is.null(error)) output_dir = getwd(), ...) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)53:
vweave_rmarkdown(...)50:
process_file(text, output)54:
engine$weave(file, quiet = quiet, encoding = enc)51:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)55:
doTryCatch(return(expr), name, parentenv, handler)52:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 56: output_dir = getwd(), ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: 57: vweave_rmarkdown(...)tryCatchList(expr, classes, parentenv, handlers)
54: 58: engine$weave(file, quiet = quiet, encoding = enc)tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)55: setwd(startdir)doTryCatch(return(expr), name, parentenv, handler) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {56: texi2pdf(file = output, clean = FALSE, quiet = quiet)tryCatchOne(expr, names, parentenv, handlers[[1L]]) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)57: } outputs <- c(outputs, output)tryCatchList(expr, classes, parentenv, handlers)}, error = function(e) {
thisOK <<- FALSE58: fails <<- c(fails, file)tryCatch({ message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", engine$weave(file, quiet = quiet, encoding = enc) file, conditionMessage(e))) setwd(startdir)}) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {59: texi2pdf(file = output, clean = FALSE, quiet = quiet)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", output <- find_vignette_product(name, by = "texi2pdf", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpU9evvi/file134485a6459e2.rds") engine = engine)
}An irrecoverable exception occurred. R is aborting now ...
outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
59: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/BMIselect.Rcheck/vign_test/BMIselect", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpU9evvi/file134485a6459e2.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from Introduction.Rmd:174-189 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `apply()`:
! dim(X) must have a positive length
---
Backtrace:
▆
1. └─BMIselect::BMI_LASSO(...)
2. └─base::lapply(...)
3. └─BMIselect (local) FUN(X[[i]], ...)
4. ├─base::unique(...)
5. ├─base::t(...)
6. └─base::sapply(...)
7. └─base::lapply(X = X, FUN = FUN, ...)
8. └─BMIselect (local) FUN(X[[i]], ...)
9. └─base::apply(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
dim(X) must have a positive length
--- failed re-building ‘Introduction.Rmd’
SUMMARY: processing the following file failed:
‘Introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64